>input_sequence_81128
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------------------------------------------------------------------ATGGCCCGCACGAA
GCAGACGGCGCGCAAGTCCACCGGCGGCAAGGCGCCGCGAAAGCAGCTGGCGACCAAGGCGGCGCGCAAGTCCGCCCCGG
CCACCGGCGGCGTGAAGAAGCCGCACCGTTTCCGCCCTGGAACCGTCGCGCTGCGCGAGATCCGCAAGTACCAGAAGAGC
ACGGAGCTGCTCATCCGCAAGCTCCCCTTCCAGCGGCTGGTGCGGGAGATCGCGCAGGACTTCAAGACGGACCTGCGCTT
CCAGAGCTCCGCCGTGTCCGCGCTGCAGGAGGCCGCCGAGGCGTACCTCGTCGGGCTCTTCGAGGACACCAACCTCTGCG
CCATCCACGCCAAGCGCGTCACCATCATGCCCAAGGACATCCAGCTCGCCCGCCGGATCCGAGGGGAGCGCGCCTAG---
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>chr2A_1_TraesCS2A01G377500
TGCCCTTATGAACTAATGCCCCTTGAACCGCAATTGTCACCGTTGAACCCTTGCACATATCTAAAGCACCTTATGCCAAA
TTTTGCCACATGACGAGAAAGCCTAACCTTACCGCTCTAAGAAGGTGGCAGGAATCTACGCCGAAGCTCCGTCGACTATA
ACCAGATGGACGAACTCGAGAAGGATTAGAGCCCGAAAGACAAACTCAAAGAAGAAAGCATCGCCATCCGCTTGAACGCC
GCACCAGTGAGGACTAAAAAAACTCTATTGTAAACTACTAATTAGTGCGGAGGCATCGGGGTTCCCT-CCCTGCCACCAG
CCGCCGGAGCGGCCGGCAGAGGGGAGGCGAATCAATGGGCTCGCCAGTGAAAGCAGGAGCAGGGAGTTTTCCTTAGCCGT
CTAGGGTGGTTAGGGGAGAAAGACGAGATTTTTTTCTTTTTCTCATAGTGACAAAATTTGAAACACTGTTGTATAGAGTT
GGC-TGTAAACCGAACATAAGAGTAAGGTTAATATTAAA-TTTCATTTCATTTTTCAAAATAATTATATAAAGCTATCTT
CAAGCTAGAGTTTTAATATAGTAAGTC-TTTTTATGAATCTTCATAAGTGAAATATGAGCATATCTTT--GATTTCTTTT
AAAATATGAAT-----AATTTAGACGAGTATAGATTCTCCCGGCAATTTGACCCACTCAACAGGCGAGAAGTGCTACCAC
GGATCATGATCCGTGGCCAGCCCCACACAAACACATCTCCACCGTCTCCCATTCCCCACGCCCGATCCAACGGCTCAGCC
GCGACGCGCTCCTCGATCCCTTCATGGCGCCATTATCCGTCCAAAGCCCG-AAATTTTCGCTCCCATTTTTCAACC-CGC
GCGCCAACCTCCAAATTCCCATCCCTACTT----AGCCATCTACCTG-CACCGCAGATCATCAGAACCCACACCGCCGTC
CCAAT--------CTCCCACCAAGAAACCACCGCACTCCCGCCCAGGCCGCCGACCTCCAGCTCCGATGGCCCGCACGAA
GCAGACGGCGCGCAAGTCCACCGGCGGCAAGGCGCCGCGAAAGCAGCTGGCGACCAAGGCGGCGCGCAAGTCCGCCCCGG
CCACCGGCGGCGTGAAGAAGCCGCACCGTTTCCGCCCTGGAACCGTCGCGCTGCGCGAGATCCGCAAGTACCAGAAGAGC
ACGGAGCTGCTCATCCGCAAGCTCCCCTTCCAGCGGCTGGTGCGGGAGATCGCGCAGGACTTCAAGACGGACCTGCGCTT
CCAGAGCTCCGCCGTGTCCGCGCTGCAGGAGGCCGCCGAGGCGTACCTCGTCGGGCTCTTCGAGGACACCAACCTCTGCG
CCATCCACGCCAAGCGCGTCACCATCATGCCCAAGGACATCCAGCTCGCCCGCCGGATCCGAGGGGAGCGCGCCTAGCCT
CCGAATGCTTCCTGCCGCCATGGTCCCTTCTTGGTTGATCCTGAGGGGATTTATTTCGTCCACCTGTGCGTCGAGTTGTT
TAGGTTCTACTAGTCGATGATATGGTCCTGTGATGTTGATTACCTATTGGGAAATTGCAATGGATGTGAATGTGATATAT
TTTATCCTCATTTCAGAGATCTGGTGAATTGAATTCTCTGCTTGGATGCTATGTCTGGTGAATGATTCTGTACCATCCTA
GGAATGGTTCT-----------------GTTTGTGTATCAGAAATTTGCAATCGACAATTACTGTGGAGATTGCAGAATT
TTGTACATGTTTGTGTGTTGTTTAATTCTTTTGAGCACCGGCTATTTTGTCTAACAGTCTGTTAACTGACAGAATGCATA
ACTTAGTGTTAACTGACAGAATGCATAATTTAGTGTTAACTGACAGAATGCATAATTTGATGTCA--------------G
ATTAAACTTTAGATAT--------GATCCCTATGAGGCTACTTCTGCCAAAGTTTTGATTGATCGGAAGGTGGATGTGAG
TACGAGCCACTCATCACCGCAGTTGCTATGATATTGTTTGTAGTTATTGTGGCATAGATCCCATCCTTGCTCACGTAGTT
CTGCGGGTCTCGGAGGACCGTCACAATTGCAAAGTTGCTGTTTACAATCTTGCTGGTGCCACACTGCACATATGGCCATA
TGGGTAAAAAAGTTTTGGCTCCGTTACCGTATCCACATCAAGCCTTGGTCCCATACTTCAGCCCTGAAATCACCACCTGA
CCAGTTTCAGTAGTAA------TTGACACTTGTAATTTCAGATAGGGTTATGAACCAAGCCAATTGATCTACTCACTCGA
TGGCAGACAGGATTTGGCAGAGCTTACCATGAGCTTCTGGGTGCCTGAACAGCTCGAGCATGACGGAATATTTGTTTTTT
TTTGCGGGTGACGGAATATTTGTTGACGTACACACAATCGATGCATCCTAAATCGTCTTCCTACCCGCGCCCAAGCAGTT
GT
>chr2D_42
-----------------------------------------GTTGAACCCTTGCATAGATCTGAAGCACCTGACACCAAA
TCTTAACACACGACGAGAAATCCTAACCTCACCACCCCAAGGAGGCGGCAGGAATCTACGCCGGAGCTCCGTCGACTTCA
ATCAGACGGATGAACTCGAGGAGGATCAGAGTCTGGAAGACAAATTCAAAGAAGAAGCG-TCGCCGTCCGCTCGAACACC
GCACCAACAAGGACTAAAAAAACCCTAACGTAAATTACTAACCAGAACGGAGTCACCGGGATTCCTCACCCCGCCACCGA
CCGTCGGAGCGGCAGGTAGAAGGG-GGCAAATCCATGGGCTCGCCAGTGAAAGCCGGAGGAAAGAGTTTTCCCTAACTGC
CTAGGGTGGTTAGCGGAGAAAAACGAGAAAAAAATTCACATT-----------AAATTTGAAACACCGCTGTATCGAGCT
GACATGTAAACCGAACATAAGAGGAAGGTTAATATTGATTTTTATTTCCTTTTTTCTAAATAACTATATAAACCTATCTC
CGAGCCAGAGTTTTGATACACTAAGTTTTTTTTATGGATCTTGATAAGTGAAATGTGAGCATATATTCCCGATATCTTTA
AAAAATATATGTGAGCAATTCAAATGAGCGTAGATTCTCCCAGCAACTTGGCCCACTCAACAGGCGAGAAGTGCTACCAC
GCATCACGATCCGT------------------------------------------------------------------
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>chr7D_699
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---------------------------------------------------------------------AGTACTCCCAC
GGATCACGATCCGTGGCCAA-CCCGCACAAGCGCATCTGCACCGTCAGT------CCATCCCTGATCTAACGTCTCACCC
AACCCCGCGCGCCCC-TCCCTCCGTGGCGCCTTCACCCCTCCCAAACCCA-AAAATTTCCGCTCCATCTCCCACCCGCGC
GCGCCATGCCCCAAATTCCCACCCCTGCTACTTAAACCCTCCGCCGCTCCCCACGAATCCTCACAACTCAGCCAGCCGCA
CCGCCCCCGCTCCCTCCCAAGAATCCCCCACCGCAGTCCCCCGGCAGCCCCCGCGCG---GCTCCGATGGCCCGCACGAA
GCAGACGGCGCGCAAGTCGACGGGCGGCAAGGCGCCGCGGAAGCAGCTGGCCACCAAGGCGGCGCGCAAGTCGGCGCCGG
CCACCGGCGGCGTGAAGAAGCCGCACCGGTTCCGCCCGGGCACCGTCGCGCTGCGCGAGATCCGCAAGTACCAGAAGAGC
ACGGAGCTGCTCATCCGCAAGCTCCCCTTCCAGCGCCTGGTGCGGGAGATCGCGCAGGACTTCAAGACGGACCTCCGGTT
CCAGAGCTCCGCCGTGTCGGCGCTGCAGGAGGCCGCCGAGGCGTACCTGGTGGGGCTGTTCGAGGACACCAACCTCTGCG
CCATCCACGCCAAGCGCGTCACCATCATGCCCAAGGACATCCAGCTCGCTCGCCGCATCCGTGGGGAGCGCGCCTAGGCC
TC------------------------------------------------------------------------------
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>chr2D_829
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---------------------------------------TCCAAAGCCCAAAAATTTTCGCTCAGAATTTTCAAAC-CGC
GCGCCATCTTCCAAATCCCCACCCCTACTT----AACCCTCCACCGCTACCC-CAAATCATCACAACCCACGCCGCCGCC
CCAAT--------CTCCCAATAAGAAACCATCGCTCGCCCGCCCAGGTCGTCGATCCCCTGCTCTAATAGCCCGCACGAA
GCAGACGACGCGCAA--------------------CGCAGAAGCAGCTGGCGACCAAGGCGGCGCGCAAGTCCGCCCCGG
TCACCGGCGGCATGAAGAAACCCCACCTTTTCCACCCGGGTACCATTGTGCTGCGCGAGATCTGGAAGTACCAGAAGAGC
ACGGAGCTTCTCATCCGCAAACTCCCCTTCCAGCGGCTGGTGCAGGAGATCGCACGGGACTACAAGACTGACTTGTGCTT
CCAGAGCTCCGCCGTGTCGGCGCTGCAGGAGGCCGCCAAGGCGTACCTCATCGGGCTCTTCGAGGACACCAACCTTTGTG
CCATCCACGCCAAGCGCGTCACCATCATGCCCAAGGACATCCTGCTCGCCCGCCGCATCCACGGGGAGCGCGCCTAGGCT
TCGAATGCTTCCTGCCCCCATGGTTCCTTGTTG----ATCTCGAGGAGATTTATTTCATCCACCTTTGCTCCGAGTTACT
ATTAGGTTG-TAGTCGATGATATGTTCCCGTGATGTTGATTACCAGTTCGAAAATTGCAATGGATGTGATC------TAT
TTTATCATTGTTTCTGAGATCTCGTGAATCAAATTATGTGCTTGGATGCTATGTTTGGTGAATGGTTCT-----------
-----------TGTTCTGGAGTTATTTTATTTGCGTATCAGAAATTTGCAATTGAGAATTACTGTGGAGATTACAAATTT
TTGTCCATGTTTGTATGTTCTTTAATTCTTTTGAGCGCCGACCATTTTATCTAACAAGCTGTTAACTGACAGAATGCATA
A---------------------------TTTGGTGTTCACTAACAAGCTACATAATTTGGTGTCAGCAACACCGTATCTG
ATTAAACTTGAGATCG--------GACCCCGATGAGGCTACTTCTGCCAAAGTTTTGAAAGATCGGAAGGTGGATGTGAG
TT--------------CTGCAGTTGCTATGATATTATTTGCAGCTTCTGTTCCATGGATTCCATTCTAGGTCTCGTAGTT
ATGTGGGTCTGTGAGGGTCGTCACACTTGCAGTGTCAGCGTTTACAATTTTGTTGGTGCCACACTGCACATGTGGCCATA
TGGGTTAAAGAGTGTAGGCTCCGTTACCGTATCCACAGCAAGCCTTTGGTTCCATAC-CAGCCCTGAAATCACCACCCGA
CCAGTTTCAGTAGTACTACTACTTGACACTTGTAATTTCATATATGGCTATAAACCAAGCCGATTGATCTACTCACTATG
TGGCAGACAGGATTTGACAGAGCTTACCATGAGCTTCCGAGTGCCTGAATAGCTTGGGCATGATGGAATATTTGT-----
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>chr2B_1206
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-------------------------------AGCAGCTGGTGCGGGAAATCATGCAGGACTACAAGACTGAGCTGCACTT
CCAGAGCTCCATCGTGTCGATGTTGCAGGAGGCCGCCGAGGCGTACCTCATCGGGCTCTTCGAGGATACCAACCTCTGCG
CCATCCACGCCAAGCGCGTCACCATCATGCCCAAGGACATCCATCTCGCCCGCCACATCCACGAGGAG--------GGCT
TCGAATGCTTCCTGCCCCCATGGTTCCTTGTTG----ACCCCTAGGGGATTTATTTCATCCACCTTTGCTTCGAGTTACT
GTTAGGTTG-TAGTTGATGATATGTTCCTATGATGTTAATTACTAGATCAAAAATTGCAAAGGATGTGATC------TAT
TTTATCCTTGTTTCTGAGATCTCGTGAATCAAATTTCGTGCTTGGATGCTATGTTTGGTGAATGATTCTCTATCATCCTA
GGAATGATTCTTGTTCTGGAGTTATTTTGTTTGCGTATCAGAAATTTGCAATTGGGAATTACCA----------------
---------TTTGTATGTTCTTTAATTCTTTTGATCGTCGGCCATTTTATCTAACAAGCTATTAACTGACAGAATGCATA
A---------------------------TTTGGTGTTCACTAATAGGATGCATAATTTGGTGTCAGCAACATCGTCTCTG
ATTAAACTTGAGATATGAGTATATGACCCCGATGAGGCTACTTCTACCAAAATTTTGAAAGATCGGAAGGTGGATGTGAT
TATGAGCCACTCATCACTGCAGTTGCTATGATATTGTTTGCAGCTTCTGTTCCATAGATTCCATCCTAGCTCTCGTACTT
CTGTGGGTCTGTGAGGATCTTCGCACTTGCAGTGTCGGTGTTTACAATCTTGTTGGTGCCACACTGCACATATGGCCATA
TGGGTTAAAAATTGGAGGCTCCGTTACCATATCCGTACCAAGCCTTTAGTTCCATACT-AGCCTTGAAATCACCACTTGA
CCAGTTTTAGTAGTACTACT-CTTGACACCTGTAATTTCAGATTTTGCTATAAACCAAGACGATTGATCTACTCACTGGA
TGGCAGACAAGATTTGACAGAGCTTACCATGAGCTTCTGAGTGCCTGAATAGCATGGGCATGACAGAATATTTGT-----
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--
>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS--------------S-S----S--------S-SS-----
-S--SS----S---------S--------S---S-S-S---S---S-----------------S-------------SS-
-S----S---S---------S-----S----S-S-S--------S-----------SSSS-----S------S----S--
------SSS--------------S---SS-----S------SS--SS-----S--S----S----SS----S------SS
---S---------S--S---S---S---S----S--------------------S----S-SS---------S--S-S-S
-------------S-------S------SSSSSS-SSSSS-SSSSSSSSSSSS-------------S-S-----S---S-
-S---------------------S------------S-S----SS--S-S------S------S--------S------S
-S---S--------S---S-S-----S---------S-----S-----------S---------S--S-----S-----S
----SSSS-SS---------S-S-S---SS-----------S----S---S-----------------------------
------S------------SS---S-----S-S-----S-------SSSSSSSSS---SS--S----S----S----S--
SSSS-SSSSSS-S-SS-----S-S-------S-S-S--S----------S------------------------------
------S--------------S-------------S--S--S---SS--S--S--S-------S-------S------S-
-------------------SS---------------------------------S-S--S--------------------
------------------S--S-----------------S----------------------------------------
-------------------------------------S--S---------------------------------------
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------------------S-------------------------------------------------------------
-------------------------------------------------------S-----S---------------S--
S---------------S-------S----S---SSSS----S---------------S-------S---S-------SS-
SSSSSSS-SS--------------S-------------------SS--S-S------------------SSSSSSSS---
--------SS----S-------S------SS----S-S----------------S--------------S--S-------
------S--------------------------S------------------S--S----------------S--S-S--
----S---------S----S----------------S-----S-----S-------SS----------------------
-SSSSSSSSSSSSSSSSSSSSSSSSSSS---S-----S---S----S------------S--------------------
---------S----------------S---S---------------------------SS--------------------
--S--------------S----------------------S--S-SS---SS-------S-------S----S-------
---S------SS-----S-------S-----SS--S-S--------------S---------------------------
-----S-------S-S---------------------S--------S-SSS-SSSSS-----------------------
---------------S----------------------------S--S---S---------S---------------S--
----------------S----------------------S---------S----S-S------------------SSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SS
>forward_38
------------------CCCCTTGAACCGCAATTGTC------------------------------------------
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>reverse_1457
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----------------GCCATGGTCCCTTCTTGGTT--------------------------------------------
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